Jan. 27th 2015

  • Goal : To identify DNA methylation markers which the difference in methylation are associated with change in PHQ (~ Aim 2)

  • Model : PHQchange = a + b * Methylation Difference + e

  • Sites : 437014

  • Sample size:

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - raw PHQchange:

  • 5% MinP Cutoff - INV PHQchange:

Association Test

PHQchange ~ Difference in Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Pos Genes pval p.adj size
cg00886598 5 42812844 SEPP1 2.0e-07 0.0765 37
cg20292653 2 5847374 NA 2.0e-07 0.1036 37
cg05518543 4 1283165 MAEA 3.0e-07 0.1280 37
cg20049415 20 21377671 NKX2-4 8.0e-07 0.3376 37
cg07432626 5 146889536 NA 1.0e-06 0.4491 37
cg10169763 16 87873389 SLC7A5 4.4e-06 1.0000 37
cg03625512 12 125569850 AACS 4.4e-06 1.0000 37
cg24601967 1 6366496 ACOT7 5.4e-06 1.0000 37
cg07678449 4 171011395 AADAT 6.5e-06 1.0000 37
cg18843062 12 132685606 GALNT9 6.7e-06 1.0000 37

Residual QQ plots top 6 sites - raw PHQchange

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Leverage Plots top 6 sites - raw PHQchange

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Cook's Distance - raw PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Difference in Methylation

QQplot: all sites

QQplot: all sites 437014 vs thinned 106586

QQplot: thinned 106586

QQplot: thinned 106586

Results based on INV PHQchange
CpG Chr Pos Genes pval p.adj size
cg20292653 2 5847374 NA 4.00e-07 0.1746 37
cg05706582 7 2566911 LFNG 5.50e-06 1.0000 37
cg09640960 20 60794676 HRH3 7.00e-06 1.0000 37
cg23026478 6 46706037 NA 1.03e-05 1.0000 37
cg00886598 5 42812844 SEPP1 1.28e-05 1.0000 37
cg10169763 16 87873389 SLC7A5 1.55e-05 1.0000 37
cg09405169 3 12329745 PPARG 3.26e-05 1.0000 37
cg14912788 1 3661862 KIAA0495 3.41e-05 1.0000 37
cg13883397 11 61900852 INCENP 3.49e-05 1.0000 37
cg12405983 19 58630240 ZSCAN18 3.69e-05 1.0000 37

Residual QQ plots top 6 sites - INV PHQchange

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## 63127 
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Leverage Plots top 6 sites - INV PHQchange

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Cook's Distance - INV PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Difference in Methylation

QQplot pvals : INV PHQchange ~ INV Diff Methyl

ScatterPlot: -log10 InvDeltaMethyl vs -log10 DeltaMethyl

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Pos Genes pval p.adj size
cg20292653 2 5847374 NA 4.00e-07 0.1579 65
cg09640960 20 60794676 HRH3 7.60e-06 1.0000 65
cg23026478 6 46706037 NA 7.60e-06 1.0000 65
cg05706582 7 2566911 LFNG 9.60e-06 1.0000 65
cg14912788 1 3661862 KIAA0495 1.72e-05 1.0000 65
cg10169763 16 87873389 SLC7A5 2.46e-05 1.0000 65
cg09405169 3 12329745 PPARG 2.71e-05 1.0000 65
cg03722909 18 42324965 SETBP1 2.85e-05 1.0000 65
cg27522060 15 65360366 RASL12 4.06e-05 1.0000 65
cg07800890 7 101889824 CUX1 4.10e-05 1.0000 65

Residual QQ plots top 6 sites

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Leverage Plots top 6 sites

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Cook's Distance

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PCA on top sites - Scree Plot

PCA on top sites - biplot